Tag clouds have become very popular as visual representations of the main topics in document sets or as navigation tools that can provide quick access to resources related with specific topics. However, their ability to represent the information environment associated with any meaningful reality in a way that is collectively visible, actionable and easily understood may also be very relevant, even when the reality being represented is no longer a set of documents or resources, but a stream of interactions occurring within a
particular ubiquitous computing environment. In this paper, we explore the use of tag clouds within the context of situated displays and services. We hypothesise that such tag clouds may have a role as dynamic
representations of place and also as interaction controls, supporting the same comprehension and navigation functions of classical tag clouds. We describe two case studies in which this concept of situated tag cloud
has been experimented in real-world settings. The case studies demonstrate two different applications of the tag cloud concept as the basis for place description and situated interaction. The results obtained from the case studies suggest that situated tag clouds can indeed provide valuable representations of place and
situations and can also support simple interaction models...

Iron affects the physiology of bacteria in two different ways: as a micronutrient for bacterial growth and as a catalyst for the formation of hydroxyl radicals. In this study, we used DNA microarrays to identify the C. jejuni genes that have their transcript abundance affected by iron availability. The transcript levels of 647 genes were affected after the addition of iron to iron-limited C. jejuni cells. Several classes of affected genes were revealed within 15 min, including immediate-early response genes as well as those specific to iron acquisition and metabolism. In contrast, only 208 genes were differentially expressed during steady-state experiments comparing iron-rich and iron-limited growth conditions. As expected, genes annotated as being involved in either iron acquisition or oxidative stress defense were downregulated during both time course and steady-state experiments, while genes encoding proteins involved in energy metabolism were upregulated. Because the level of protein glycosylation increased with iron limitation, iron may modulate the level of C. jejuni virulence by affecting the degree of protein glycosylation. Since iron homeostasis has been shown to be Fur regulated in C. jejuni, an isogenic fur mutant was used to define the Fur regulon by transcriptome profiling. A total of 53 genes were Fur regulated...

Cardiac remodelling with interstitial fibrosis in renal failure, which so far is only poorly understood on the molecular level, was investigated in the rat model by a global
gene expression profiling analysis. Sprague–Dawley rats were subjected to subtotal
nephrectomy (SNX) or sham operation (sham) and followed for 2 and 12 weeks,
respectively. Heart-specific gene expression profiling, with RZPD Rat Unigene-1
cDNA arrays containing about 27 000 gene and EST sequences revealed substantial
changes in gene expression in SNX compared to sham animals. Motor protein genes,
growth and differentiation markers, and extracellular matrix genes were upregulated
in SNX rats. Obviously, not only genes involved in cardiomyocyte hypertrophy, but
also genes involved in the expansion of non-vascular interstitial tissue are activated
very early in animals with renal failure. Together with earlier findings in the SNX
model, the present data suggest the hypothesis that the local renin–angiotensin system
(RAS) may be activated by at least two pathways: (a) via second messengers and Gproteins
(short-term signalling); and (b) via motor proteins, actins and integrins (longterm
signalling). The study documents that complex hybridization analysis yields
reproducible and promising results of patterns of gene activation pointing to signalling
pathways involved in cardiac remodelling in renal failure. The complete array data
are available via http://www.rzpd.de/cgi-bin/services/exp/viewExpressionData.pl.cgi

Although the JAK/STAT pathway regulates numerous processes in vertebrates and invertebrates through modulating transcription, its functionally-relevant transcriptional targets remain largely unknown. With one jak and one stat (stat92E), Drosophila provides a powerful system for finding new JAK/STAT target genes. Genome-wide expression profiling on eye discs in which Stat92E is hyperactivated, revealed 584 differentially-regulated genes, including known targets domeless, socs36E and wingless. Other differentially-regulated genes (chinmo, lama, Mo25, Imp-L2, Serrate, Delta) were validated and may represent new Stat92E targets. Genetic experiments revealed that Stat92E cell-autonomously represses Serrate, which encodes a Notch ligand. Loss of Stat92E led to de-repression of Serrate in the dorsal eye, resulting in ectopic Notch signaling and aberrant eye growth there. Thus, our micro-array documents a new Stat92E target gene and a previously-unidentified inhibitory action of Stat92E on Notch signaling. These data suggest that this study will be a useful resource for the identification of additional Stat92E targets.

Global analysis of stem/progenitor cells promises new insight into mechanisms that govern self-renewal and cellular potential, an unresolved question of stem/progenitor cell biology. Despite rapid advance of genome-wide profiling methods, the difficulty in cell purification remains a major challenge for global analysis of somatic stem/progenitor cells. Genetic tagging with a reporter provides a powerful tool for identification and isolation of a specific mature cell type, however, for stem/progenitor cells, reporter retention by progeny may be a concern for impurity. Here we describe a genetic system combining a progenitor cell specific label with a second tag for marking differentiation. We present evidence that differential labeling of neural progenitor cells and their progeny enables prospective purification of these two cell types, whereas isolation based on a single marker compromises the purity of the intended progenitor population. Comparative expression profiling between the purified progenitors and progeny documents a neural progenitor cell transcriptome and uncovers an important role of TAM receptor tyrosine kinases in the maintenance of neural progenitor cells. This study establishes a general strategy for isolation of somatic stem/progenitor cells and provides a transcriptome database of neural progenitor cells useful for identification of causal factors of neural progenitor cell state...

Through domestication, humans have substantially altered the morphology of Zea mays ssp. parviglumis (teosinte) into the currently recognizable maize. This system serves as a model for studying adaptation, genome evolution, and the genetics and evolution of complex traits. To examine how domestication has reshaped the transcriptome of maize seedlings, we used expression profiling of 18,242 genes for 38 diverse maize genotypes and 24 teosinte genotypes. We detected evidence for more than 600 genes having significantly different expression levels in maize compared with teosinte. Moreover, more than 1,100 genes showed significantly altered coexpression profiles, reflective of substantial rewiring of the transcriptome since domestication. The genes with altered expression show a significant enrichment for genes previously identified through population genetic analyses as likely targets of selection during maize domestication and improvement; 46 genes previously identified as putative targets of selection also exhibit altered expression levels and coexpression relationships. We also identified 45 genes with altered, primarily higher, expression in inbred relative to outcrossed teosinte. These genes are enriched for functions related to biotic stress and may reflect responses to the effects of inbreeding. This study not only documents alterations in the maize transcriptome following domestication...

Adenoid cystic carcinoma (ACC), a relatively rare malignancy usually of salivary gland origin, has a signature v-myb avian myeloblastosis viral oncogene homolog–nuclear factor I/B (MYB-NFIB) gene fusion that activates MYB transcriptional regulatory activity. A new study in this issue by Stephens et al. is a comprehensive genomic mutation profiling analysis of this neoplasm and documents a common theme of alteration in chromatin regulatory genes. Also, mutations in SPEN (split ends, homolog of Drosophila), which encodes an RNA-binding coregulatory protein, suggest that other changes in transcriptional regulation may involve the NOTCH, FGFR, or other signaling pathways in which SPEN participates. Since there is a low prevalence of mutations in common oncogenes and tumor-suppressor genes, it is likely that alterations primarily in specific transcriptional regulatory genes, augmented by changes in chromatin structure, drive the neoplastic process in ACC.

The first documents mentioning Jewish people in Iberia are from the Visigothic period. It was also in this period that the first documented anti-Judaic persecution took place. Other episodes of persecution would happen again and again during the long troubled history of the Jewish people in Iberia and culminated with the Decrees of Expulsion and the establishment of the Inquisition: some Jews converted to Catholicism while others resisted and were forcedly baptized, becoming the first Iberian Crypto-Jews. In the 18th century the official discrimination and persecution carried out by the Inquisition ended and several Jewish communities emerged in Portugal. From a populational genetics point of view, the worldwide Diaspora of contemporary Jewish communities has been intensely studied. Nevertheless, very little information is available concerning Sephardic and Iberian Crypto-Jewish descendants. Data from the Iberian Peninsula, the original geographic source of Sephardic Jews, is limited to two populations in Portugal, Belmonte, and Bragança district, and the Chueta community from Mallorca. Belmonte was the first Jewish community studied for uniparental markers. The construction of a reference model for the history of the Portuguese Jewish communities...

A system that recognises cross-lingual plagiarism needs to establish – among other things – whether two pieces of text written in different languages are equivalent to each other. Potthast et al. (2010) give a thorough overview of this challenging task. While the Joint Research Centre (JRC) is not specifically concerned with plagiarism, it has been working for many years on developing other cross-lingual functionalities that may well be useful for the plagiarism detection task, i.e. (a) cross-lingual document similarity calculation, (b) subject domain profiling of documents in many different languages according to the same multilingual subject domain categorisation scheme, and (c) the recognition of name spelling variants for the same entity, both within the same language and across different languages and scripts. The speaker will explain the algorithms behind these software tools and he will present a number of freely available language resources that can be used to develop software with cross-lingual functionality.; JRC.G.2-Global security and crisis management

One of the ultimate goals of natural language
processing (NLP) systems is understanding the
meaning of what is being transmitted, irrespective of
the medium (e.g., written versus spoken) or the form
(e.g., static documents versus dynamic dialogues).
Although much work has been done in traditional
language domains such as speech and static written
text, little has yet been done in the newer
communication domains enabled by the Internet, e.g.,
online chat and instant messaging. This is in part due
to the fact that there are no annotated chat corpora
available to the broader research community. The
purpose of this research is to build a chat corpus,
tagged with lexical (token part-of-speech labels),
syntactic (post parse tree), and discourse (post
classification) information. Such a corpus can then be
used to develop more complex, statistical-based NLP
applications that perform tasks such as author
profiling, entity identification, and social network
analysis.

The bibliographic profile of 125 undergraduate (licentiate) theses was analyzed, describing absolute quantities of several bibliometric variables, as well as within-document indexes and average lags of the references. The results show a consistent pattern across the years in the 6 cohorts included in the sample (2001-2007), with variations, which fall within the robust confi dence intervals for the global central tendency. The median number of references per document was 52 (99% CI 47-55); the median percentage of journal articles cited was 55%, with a median age for journal references of 9 years. Other highlights of the bibliographic profile were the use of foreign language references (median 61%), and low reliance on open web documents (median 2%). A cluster analysis of the bibliometric indexes resulted in a typology of 2 main profiles, almost evenly distributed, one of them with the makeup of a natural science bibliographic profile and the second within the style of the humanities. In general, the number of references, proportion of papers, and age of the references are close to PhD dissertations and Master theses, setting a rather high standard for undergraduate theses.; Se analizó el perfil bibliográfico de 125 tesis de grado (licenciatura)...

Cancer of Cowper's gland is a very rare cancer. This case represents the 9th case in the medical literature. As such, there are no phase II or phase III trials to guide treatment. In this article, we report the successful treatment of a patient over a 7-year period guided solely by molecular profiling. Through multiple cycles to treatment, the cancer was controlled using drugs targeting c-kit, as the cancer steadily increased the expression of c-kit. This report also documents the use of a novel drug combination based on sunitinib that was well tolerated and may warrant testing in other c-kit-dependent cancers.

Personalization is being applied to great extend in many systems. This paper
presents a multi-dimensional user data model and its application in web search.
Online and Offline activities of the user are tracked for creating the user
model. The main phases are identification of relevant documents and the
representation of relevance and similarity of the documents. The concepts
Keywords, Topics, URLs and clusters are used in the implementation. The
algorithms for profiling, grading and clustering the concepts in the user model
and algorithm for determining the personalized search results by re-ranking the
results in a search bank are presented in this paper. Simple experiments for
evaluation of the model and their results are described.; Comment: 6 pages, 3 figures -"Published with International Journal of Computer
Applications (IJCA)"